Six of the 20 highest-paid private college presidents in the country hailed from New York state schools in 2010 — including four in Manhattan, according to a new report by The Chronicle of Higher Education.

Leading the charge was then-retiring New School chief Bob Kerrey — whose compensation soared just past $3 million in his final year running the university.

His payout after a decade at the helm included a $1.2 million bonus on top of a base salary of roughly $600,000.

”Under his leadership, the university’s student body grew by nearly 50 percent and freshman applications climbed 94 percent,” a spokesman said of the trustees’ decision to award Kerrey the hefty bonus.

BOB KERREY Highest-paid college head.

Rensselaer Polytechnic Institute President Shirley Ann Jackson was the second highest-paid higher ed honcho nationally, taking home over $2.3 million in compensation.

Bob Kerrey No. 1 on list of highest-paid private college presidents

THE ASSOCIATED PRESS

Compensation for private college presidents has continued to drift upward, while the number crossing the $1 million barrier, a signal of prestige, and a magnet for criticism, held steady at 36, according to a new survey.

The latest annual compilation by The Chronicle of Higher Education covers data from 2010, due to lag time in the release of federal tax information. That year, median compensation for the 494 presidents in the survey, leaders of institutions with budgets of at least $50 million, was $396,649, or 2.8 percent higher than in last year’s survey. But median base salary fell slightly, by less than 1 percent.

The highest paid was Bob Kerrey, who was president of The New School in New York until December, 2010 before returning to Nebraska, where he made an unsuccessful run to return to the U.S Senate. Kerrey’s total compensation over more than $3 million. His base salary was just over $600,000, but he received a $1.2 million retention bonus and more than $620,000 in deferred compensation.

It is common for such payments to inflate compensation for presidents in their final year in a position. Three presidents in 2010’s top 10 are no longer at those institutions: Kerrey, David Pollick of Birmingham-Southern College, and Steven Sample of the University of Southern California.

The highest-paid in 2010 who remains on the job is Shirley Ann Jackson of Rensselaer Polytechnic Institute in New York, who was No. 2 at $2.34 million, followed by Pollick, at $2.31 million. The highest base salary belonged to John Sexton of New York University and totaled $1.24 million out of $1.48 million total compensation.

The Chronicle has previously compiled salary data for the presidents of public institutions, which was available for 2011. Those figures showed three public university presidents earned more than $1 million in 2011, led by Gordon Gee of Ohio State with total compensation of just under $2 million.

Then there’s the other end of the scale – presidents of roughly two dozen Roman Catholic institutions including Villanova University, Boston College, Marquette and a number of smaller schools, whose compensation is zero. All are either clergy or members of religious orders.

The Chronicle reports this year that half the institutions that employed the 50 highest-paid college presidents in 2010 used a practice called “grossing up,” adding additional cash and benefits to compensation packages to make up for the taxes recipients pay. The practice has been largely abandoned at publicly traded companies due to shareholder criticism, but appears alive and well in the nonprofit sector.